Starting phenix.real_space_refine on Tue Sep 24 04:59:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/09_2024/7dhr_30682.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/09_2024/7dhr_30682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/09_2024/7dhr_30682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/09_2024/7dhr_30682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/09_2024/7dhr_30682.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhr_30682/09_2024/7dhr_30682.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4538 2.51 5 N 1206 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7057 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1495 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 5 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2301 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 169 Chain: "G" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 317 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 851 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2078 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.73, per 1000 atoms: 0.67 Number of scatterers: 7057 At special positions: 0 Unit cell: (82.134, 98.358, 120.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1271 8.00 N 1206 7.00 C 4538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 29.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.592A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.755A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.952A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 331 through 345 removed outlier: 3.516A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.819A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 350' Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.914A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.721A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.697A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.918A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 31 through 49 removed outlier: 3.520A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 71 through 76 Processing helix chain 'R' and resid 77 through 86 removed outlier: 4.055A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 93 removed outlier: 3.615A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 88 through 93' Processing helix chain 'R' and resid 105 through 116 removed outlier: 3.634A pdb=" N THR R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 136 removed outlier: 3.523A pdb=" N ALA R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 198 through 203 Processing helix chain 'R' and resid 213 through 218 Processing helix chain 'R' and resid 219 through 221 No H-bonds generated for 'chain 'R' and resid 219 through 221' Processing helix chain 'R' and resid 222 through 227 Processing helix chain 'R' and resid 228 through 237 removed outlier: 4.395A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 286 removed outlier: 3.785A pdb=" N ALA R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 281 through 286' Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.504A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 316 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.762A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.623A pdb=" N TYR R 326 " --> pdb=" O ASN R 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 326' Processing helix chain 'R' and resid 329 through 336 removed outlier: 3.663A pdb=" N ARG R 333 " --> pdb=" O SER R 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE R 334 " --> pdb=" O PRO R 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.711A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.509A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.550A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.759A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 153 removed outlier: 6.870A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.519A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 removed outlier: 4.826A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.720A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.619A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 21 Processing sheet with id=AB2, first strand: chain 'N' and resid 36 through 39 164 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2272 1.34 - 1.46: 1719 1.46 - 1.58: 3153 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 7202 Sorted by residual: bond pdb=" C VAL R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.89e+00 bond pdb=" C LEU R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.97e+00 bond pdb=" N THR R 189 " pdb=" CA THR R 189 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.54e-02 4.22e+03 2.23e+00 bond pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 1.458 1.476 -0.017 1.35e-02 5.49e+03 1.66e+00 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9490 1.94 - 3.88: 277 3.88 - 5.81: 55 5.81 - 7.75: 11 7.75 - 9.69: 8 Bond angle restraints: 9841 Sorted by residual: angle pdb=" N VAL R 152 " pdb=" CA VAL R 152 " pdb=" C VAL R 152 " ideal model delta sigma weight residual 111.81 107.54 4.27 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER N 112 " pdb=" N THR N 113 " pdb=" CA THR N 113 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.42 108.46 4.96 1.17e+00 7.31e-01 1.80e+01 angle pdb=" C ARG R 304 " pdb=" N LYS R 305 " pdb=" CA LYS R 305 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 129.23 -5.76 1.53e+00 4.27e-01 1.42e+01 ... (remaining 9836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3746 17.38 - 34.76: 340 34.76 - 52.14: 70 52.14 - 69.51: 8 69.51 - 86.89: 4 Dihedral angle restraints: 4168 sinusoidal: 1330 harmonic: 2838 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 -11.85 -74.15 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CA ASN R 51 " pdb=" C ASN R 51 " pdb=" N VAL R 52 " pdb=" CA VAL R 52 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA SER R 137 " pdb=" C SER R 137 " pdb=" N PRO R 138 " pdb=" CA PRO R 138 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 977 0.064 - 0.128: 175 0.128 - 0.191: 26 0.191 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CB ILE R 303 " pdb=" CA ILE R 303 " pdb=" CG1 ILE R 303 " pdb=" CG2 ILE R 303 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE R 153 " pdb=" CA ILE R 153 " pdb=" CG1 ILE R 153 " pdb=" CG2 ILE R 153 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1177 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO R 323 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO B 236 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO R 211 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.037 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2471 2.84 - 3.36: 5803 3.36 - 3.87: 10703 3.87 - 4.39: 11913 4.39 - 4.90: 21258 Nonbonded interactions: 52148 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.329 3.040 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.336 3.040 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.343 3.040 nonbonded pdb=" OG SER R 207 " pdb=" OAC 5FW R 601 " model vdw 2.349 3.040 nonbonded pdb=" O PHE R 133 " pdb=" OG SER R 137 " model vdw 2.352 3.040 ... (remaining 52143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.970 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7202 Z= 0.262 Angle : 0.858 9.691 9841 Z= 0.470 Chirality : 0.052 0.319 1180 Planarity : 0.006 0.072 1240 Dihedral : 14.285 86.892 2318 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.06 % Favored : 90.83 % Rotamer: Outliers : 0.31 % Allowed : 9.71 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.33 (0.18), residues: 949 helix: -5.10 (0.08), residues: 306 sheet: -3.66 (0.31), residues: 191 loop : -3.70 (0.22), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.002 PHE N 27 TYR 0.017 0.001 TYR B 59 ARG 0.005 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7889 (tttt) cc_final: 0.7687 (tttt) REVERT: A 343 ASP cc_start: 0.8084 (t70) cc_final: 0.7840 (t70) REVERT: B 99 TRP cc_start: 0.7046 (m-90) cc_final: 0.6773 (m-90) REVERT: R 279 MET cc_start: 0.8099 (tpt) cc_final: 0.7884 (tpt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2198 time to fit residues: 39.7353 Evaluate side-chains 112 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 28 optimal weight: 0.0010 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 278 ASN A 384 GLN A 390 GLN B 183 HIS B 239 ASN B 266 HIS B 295 ASN G 24 ASN R 65 GLN R 229 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7202 Z= 0.125 Angle : 0.533 5.564 9841 Z= 0.288 Chirality : 0.042 0.145 1180 Planarity : 0.004 0.058 1240 Dihedral : 5.461 59.717 1034 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.31 % Allowed : 14.95 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.20), residues: 949 helix: -4.25 (0.16), residues: 321 sheet: -3.53 (0.29), residues: 187 loop : -3.32 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 93 PHE 0.015 0.001 PHE N 29 TYR 0.010 0.001 TYR B 59 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7390 (ttp-110) cc_final: 0.7137 (ttp-110) REVERT: R 38 ILE cc_start: 0.8198 (mt) cc_final: 0.7977 (mt) REVERT: R 156 MET cc_start: 0.6638 (ttm) cc_final: 0.6384 (tmm) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.1884 time to fit residues: 32.9524 Evaluate side-chains 111 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 390 GLN B 183 HIS B 225 HIS G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7202 Z= 0.176 Angle : 0.526 5.608 9841 Z= 0.285 Chirality : 0.042 0.126 1180 Planarity : 0.004 0.052 1240 Dihedral : 5.338 57.313 1034 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.62 % Allowed : 17.26 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.22), residues: 949 helix: -3.66 (0.20), residues: 327 sheet: -3.37 (0.29), residues: 196 loop : -3.08 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.026 0.001 PHE A 212 TYR 0.010 0.001 TYR B 59 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.783 Fit side-chains REVERT: B 258 ASP cc_start: 0.7827 (m-30) cc_final: 0.6774 (t0) REVERT: R 38 ILE cc_start: 0.8277 (mt) cc_final: 0.8006 (mt) REVERT: R 156 MET cc_start: 0.6738 (ttm) cc_final: 0.6384 (tmm) outliers start: 17 outliers final: 9 residues processed: 120 average time/residue: 0.2018 time to fit residues: 32.2078 Evaluate side-chains 112 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 216 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 24 optimal weight: 0.0980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7202 Z= 0.139 Angle : 0.498 5.558 9841 Z= 0.270 Chirality : 0.041 0.132 1180 Planarity : 0.003 0.050 1240 Dihedral : 4.989 55.365 1034 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.77 % Allowed : 17.87 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.23), residues: 949 helix: -3.25 (0.23), residues: 327 sheet: -3.16 (0.31), residues: 189 loop : -2.88 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE A 212 TYR 0.006 0.001 TYR A 358 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.748 Fit side-chains REVERT: A 270 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8256 (tt) REVERT: R 38 ILE cc_start: 0.8312 (mt) cc_final: 0.8039 (mt) REVERT: R 156 MET cc_start: 0.6670 (ttm) cc_final: 0.6349 (tmm) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.2126 time to fit residues: 34.5310 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 0.0070 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 23 optimal weight: 0.0670 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN B 183 HIS G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7202 Z= 0.114 Angle : 0.477 5.592 9841 Z= 0.258 Chirality : 0.041 0.136 1180 Planarity : 0.003 0.049 1240 Dihedral : 4.506 49.716 1034 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.08 % Allowed : 18.95 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.24), residues: 949 helix: -2.90 (0.25), residues: 328 sheet: -2.91 (0.32), residues: 189 loop : -2.68 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.006 0.001 TYR A 358 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7323 (mppt) cc_final: 0.6997 (mmtm) REVERT: A 270 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8300 (tt) REVERT: B 45 MET cc_start: 0.8111 (mtm) cc_final: 0.7877 (mtm) REVERT: N 60 TYR cc_start: 0.8317 (m-80) cc_final: 0.7723 (m-80) REVERT: R 38 ILE cc_start: 0.8321 (mt) cc_final: 0.8090 (mt) REVERT: R 156 MET cc_start: 0.6465 (ttm) cc_final: 0.6183 (tmm) REVERT: R 220 SER cc_start: 0.7999 (m) cc_final: 0.7798 (t) outliers start: 20 outliers final: 13 residues processed: 128 average time/residue: 0.1948 time to fit residues: 33.3435 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 225 HIS G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7202 Z= 0.146 Angle : 0.499 5.545 9841 Z= 0.267 Chirality : 0.042 0.136 1180 Planarity : 0.003 0.047 1240 Dihedral : 4.495 44.590 1034 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.08 % Allowed : 19.88 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.25), residues: 949 helix: -2.64 (0.26), residues: 328 sheet: -2.85 (0.32), residues: 189 loop : -2.56 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 82 HIS 0.008 0.001 HIS B 225 PHE 0.024 0.001 PHE A 212 TYR 0.006 0.001 TYR A 358 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 45 MET cc_start: 0.8142 (mtm) cc_final: 0.7896 (mtm) REVERT: N 60 TYR cc_start: 0.8292 (m-80) cc_final: 0.7632 (m-80) REVERT: R 38 ILE cc_start: 0.8344 (mt) cc_final: 0.8078 (mt) REVERT: R 220 SER cc_start: 0.8109 (m) cc_final: 0.7878 (t) outliers start: 20 outliers final: 13 residues processed: 121 average time/residue: 0.1749 time to fit residues: 28.9303 Evaluate side-chains 113 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 0.0050 chunk 77 optimal weight: 0.0570 chunk 51 optimal weight: 0.0060 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7202 Z= 0.123 Angle : 0.502 10.030 9841 Z= 0.262 Chirality : 0.041 0.135 1180 Planarity : 0.003 0.046 1240 Dihedral : 4.262 38.791 1034 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.77 % Allowed : 20.34 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.25), residues: 949 helix: -2.39 (0.27), residues: 328 sheet: -2.60 (0.32), residues: 194 loop : -2.56 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.021 0.001 PHE A 212 TYR 0.006 0.001 TYR A 358 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8191 (tt) REVERT: N 60 TYR cc_start: 0.8289 (m-80) cc_final: 0.7626 (m-80) REVERT: R 38 ILE cc_start: 0.8268 (mt) cc_final: 0.7986 (mt) REVERT: R 279 MET cc_start: 0.6768 (tpt) cc_final: 0.6536 (ttt) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 0.1692 time to fit residues: 28.1140 Evaluate side-chains 112 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.3980 chunk 27 optimal weight: 0.0870 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.0670 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7202 Z= 0.120 Angle : 0.510 9.988 9841 Z= 0.261 Chirality : 0.041 0.138 1180 Planarity : 0.003 0.045 1240 Dihedral : 4.135 32.604 1034 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.77 % Allowed : 21.11 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.25), residues: 949 helix: -2.18 (0.28), residues: 324 sheet: -2.49 (0.33), residues: 195 loop : -2.43 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.020 0.001 PHE A 212 TYR 0.005 0.001 TYR A 358 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8267 (tt) REVERT: N 60 TYR cc_start: 0.8253 (m-80) cc_final: 0.7599 (m-80) REVERT: R 38 ILE cc_start: 0.8306 (mt) cc_final: 0.8024 (mt) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.1753 time to fit residues: 28.2249 Evaluate side-chains 118 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0020 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 227 GLN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7202 Z= 0.140 Angle : 0.509 9.499 9841 Z= 0.263 Chirality : 0.042 0.133 1180 Planarity : 0.003 0.044 1240 Dihedral : 4.150 27.916 1034 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.08 % Allowed : 21.26 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.25), residues: 949 helix: -2.07 (0.28), residues: 324 sheet: -2.23 (0.35), residues: 185 loop : -2.49 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE A 212 TYR 0.005 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8275 (tt) REVERT: B 45 MET cc_start: 0.8400 (mpp) cc_final: 0.7910 (mtm) REVERT: N 60 TYR cc_start: 0.8295 (m-80) cc_final: 0.7628 (m-80) REVERT: N 83 MET cc_start: 0.5770 (tpt) cc_final: 0.5424 (tpt) REVERT: R 38 ILE cc_start: 0.8324 (mt) cc_final: 0.8039 (mt) outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.1658 time to fit residues: 27.4189 Evaluate side-chains 118 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 227 GLN G 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7202 Z= 0.179 Angle : 0.533 9.093 9841 Z= 0.278 Chirality : 0.042 0.135 1180 Planarity : 0.003 0.044 1240 Dihedral : 4.421 25.958 1034 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.93 % Allowed : 22.03 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.26), residues: 949 helix: -1.99 (0.28), residues: 320 sheet: -2.36 (0.34), residues: 190 loop : -2.37 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.030 0.001 PHE N 103 TYR 0.007 0.001 TYR N 32 ARG 0.004 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8286 (tt) REVERT: N 83 MET cc_start: 0.5574 (tpt) cc_final: 0.5321 (tpt) REVERT: R 38 ILE cc_start: 0.8376 (mt) cc_final: 0.8091 (mt) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.1642 time to fit residues: 27.9667 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.0770 chunk 11 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.172489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140169 restraints weight = 7644.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141845 restraints weight = 6138.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143280 restraints weight = 5252.575| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7202 Z= 0.120 Angle : 0.503 9.319 9841 Z= 0.260 Chirality : 0.041 0.136 1180 Planarity : 0.003 0.046 1240 Dihedral : 4.041 22.414 1034 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.47 % Allowed : 22.80 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.26), residues: 949 helix: -1.78 (0.29), residues: 322 sheet: -2.16 (0.36), residues: 181 loop : -2.35 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 82 HIS 0.003 0.000 HIS A 220 PHE 0.018 0.001 PHE A 212 TYR 0.006 0.001 TYR A 358 ARG 0.004 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.15 seconds wall clock time: 30 minutes 10.27 seconds (1810.27 seconds total)